Interpretable factor models of single-cell RNA-seq via variational autoencoders von Svensson, Valentine, Gayoso, Adam, Yosef, Nir, Pachter, Lior

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Cell2location maps fine-grained cell types in spatial transcriptomics von Kleshchevnikov, Vitalii, Shmatko, Artem, Dann, Emma, Aivazidis, Alexander, King, Hamish W., Li, Tong, Elmentaite, Rasa, Lomakin, Artem, Kedlian, Veronika, Gayoso, Adam, Jain, Mika Sarkin, Park, Jun Sung, Ramona, Lauma, Tuck, Elizabeth, Arutyunyan, Anna, Vento-Tormo, Roser, Gerstung, Moritz, James, Louisa, Stegle, Oliver, Bayraktar, Omer Ali

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Joint probabilistic modeling of single-cell multi-omic data with totalVI von Gayoso, Adam, Steier, Zoë, Lopez, Romain, Regier, Jeffrey, Nazor, Kristopher L., Streets, Aaron, Yosef, Nir

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Mapping single-cell data to reference atlases by transfer learning von Lotfollahi, Mohammad, Naghipourfar, Mohsen, Luecken, Malte D., Khajavi, Matin, Büttner, Maren, Wagenstetter, Marco, Avsec, Žiga, Gayoso, Adam, Yosef, Nir, Interlandi, Marta, Rybakov, Sergei, Misharin, Alexander V., Theis, Fabian J.

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Characterization of cell fate probabilities in single-cell data with Palantir von Setty, Manu, Kiseliovas, Vaidotas, Levine, Jacob, Gayoso, Adam, Mazutis, Linas, Pe’er, Dana

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Enhancing scientific discoveries in molecular biology with deep generative models von Lopez, Romain, Gayoso, Adam, Yosef, Nir

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A Python library for probabilistic analysis of single-cell omics data von Gayoso, Adam, Lopez, Romain, Xing, Galen, Boyeau, Pierre, Valiollah Pour Amiri, Valeh, Hong, Justin, Wu, Katherine, Jayasuriya, Michael, Mehlman, Edouard, Langevin, Maxime, Liu, Yining, Samaran, Jules, Misrachi, Gabriel, Nazaret, Achille, Clivio, Oscar, Xu, Chenling, Ashuach, Tal, Gabitto, Mariano, Lotfollahi, Mohammad, Svensson, Valentine, da Veiga Beltrame, Eduardo, Kleshchevnikov, Vitalii, Talavera-López, Carlos, Pachter, Lior, Theis, Fabian J., Streets, Aaron, Jordan, Michael I., Regier, Jeffrey, Yosef, Nir

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An empirical Bayes method for differential expression analysis of single cells with deep generative models von Boyeau, Pierre, Regier, Jeffrey, Gayoso, Adam, Jordan, Michael I, Lopez, Romain, Yosef, Nir

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Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells von Gayoso, Adam, Weiler, Philipp, Lotfollahi, Mohammad, Klein, Dominik, Hong, Justin, Streets, Aaron, Theis, Fabian J., Yosef, Nir

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The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans von Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles K F, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Vorperian, Sevahn K, Wang, Wanxin

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PeakVI: A deep generative model for single-cell chromatin accessibility analysis von Ashuach, Tal, Reidenbach, Daniel A., Gayoso, Adam, Yosef, Nir

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Cell types of origin of the cell-free transcriptome von Vorperian, Sevahn K., Moufarrej, Mira N., Quake, Stephen R.

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Author Correction: Characterization of cell fate probabilities in single-cell data with Palantir von Setty, Manu, Kiseliovas, Vaidotas, Levine, Jacob, Gayoso, Adam, Mazutis, Linas, Pe’er, Dana

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The scverse project provides a computational ecosystem for single-cell omics data analysis von Virshup, Isaac, Bredikhin, Danila, Heumos, Lukas, Palla, Giovanni, Sturm, Gregor, Gayoso, Adam, Kats, Ilia, Koutrouli, Mikaela, Berger, Bonnie, Pe’er, Dana, Regev, Aviv, Teichmann, Sarah A., Finotello, Francesca, Wolf, F. Alexander, Yosef, Nir, Stegle, Oliver, Theis, Fabian J.

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Publisher Correction: Cell types of origin of the cell-free transcriptome von Vorperian, Sevahn K., Moufarrej, Mira N., Quake, Stephen R.

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The scverse project provides a computational ecosystem for single-cell omics data analysis von Virshup, Isaac, Bredikhin, Danila, Heumos, Lukas, Palla, Giovanni, Sturm, Gregor, Gayoso, Adam, Kats, Ilia, Koutrouli, Mikaela, Berger, Bonnie, Pe'er, Dana, Regev, Aviv, Teichmann, Sarah A, Finotello, Francesca, Wolf, F Alexander, Yosef, Nir, Stegle, Oliver, Theis, Fabian J

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Stress-Adaptive Responses Associated with High-Level Carbapenem Resistance in KPC-Producing Klebsiella pneumoniae von Adams-Sapper, Sheila, Riley, Lee W., Gayoso, Adam

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FUCCI U2OS cells von Weiler, Philipp, Gayoso, Adam

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FUCCI RPE1 cells von Weiler, Philipp, Gayoso, Adam

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PBMCs von Weiler, Philipp, Gayoso, Adam

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